MCCCD Program Description

General Genetics

Course: BIO240

First Term: 2005 Spring

Lecture 4 Credit(s) 4 Period(s) 4 Load
Subject Type: Academic
Load Formula: S

Description: Intensive introduction to the field of genetics including historical perspective, Mendelian insights and patterns of inheritance, exceptions to expected Mendelian ratios, quantitative genetics, non-Mendelian inheritance, pedigree analysis, molecular levels of gene expression, genetic control of metabolic pathways, analytic dissection of molecular mechanisms behind DNA replication, transcription, translation, and gene regulation in both prokaryotes and eukaryotes, population genetics, genetics of behavior, and genetics of evolution and speciation.

MCCCD Official Course Competencies
1. Describe and interpret classic experiments revealing DNA as the hereditary material and model of DNA semi-conservative replication (Griffith; Hershey-Chase; Meselson-Stahl). (I) 2. Describe the structure of nucleotides and the structure of DNA based upon the Watson-Crick model. (I) 3. Describe the process of DNA replication in prokaryotes and eukaryotes including major steps required, the proteins and enzymes involved and their specific functions, the functions of different DNA polymerases, phosphodiester bonding and deoxyribonucleoside triphosphates, several key subcomponents of DNA polymerase and their functions, and distinct processes in eukaryotes versus prokaryotes. (I) 4. Analyze and interpret potential effects of non-function mutations in replicon origin sequences and genes coding for proteins, enzymes, polymerases, and polymerase subcomponents on the process of replication. (I) 5. Describe the central dogma of gene expression. (I) 6. Describe the process of transcription initiation in prokaryotes and eukaryotes with specific reference to the functions of promoter regions, basal and proximal elements, transcription factors, RNA polymerases, formation of transcription initiation complexes, activators-enhancers, and repressors-silencers. (I) 7. Describe the process of transcription elongation in prokaryotes and eukaryotes with specific reference to catalyzing phosphodiester bonds using ribonucleoside triphosphates, and transcriptional specialization of RNA polymerases in eukaryotes. (I) 8. Describe the process of transcription termination in prokaryotes and eukaryotes with specific reference to known mechanisms. (I) 9. Describe the basic organization of mRNA transcripts and functions of leader sequences, structural/coding regions, and trailer sequences. (I) 10. Describe mechanisms of mRNA editing in eukaryotes including 5` 7-methylguanosine capping, 3` poly-A tail, exons, introns and intron terminal sequences, spliceosomes, ribozymes, substitution and insertion/deletion editing, and alternative exon splicing. (I) 11. Describe the process of translation initiation in prokaryotes and eukaryotes with reference to formation of initiation complexes, different start codon-aminoacyl tRNA mechanisms in prokaryotes and eukaryotes, Shine-Delgarno and Kozak sequences, and GTP mediated generation of 70S and 80S initiation complexes. (I) 12. Describe the structure of ribosomes and their P, A, and E sites. (I) 13. Describe the process of translation elongation in prokaryotes and eukaryotes including charging tRNAs, characteristics of the Genetic Code, function of anticodons and the wobble hypothesis, function of peptidyl transferase, Ef (or eEf) \226 GTP mediated translocation. (I) 14. Describe the mechanisms of translation termination including GTP-dependent release factor and actions and polypeptide cleavage. (I) 15. Explain gene control of proteins referencing multiple levels of protein structure, and relationship between structure and function citing specific examples of mutation effects on protein structure and function. (I) 16. Explain mutation effects on linear process of gene expression and predicted phenotypic results with reference to point and frameshift mutations (I) 17. Identify metabolic pathways of microorganisms from data on survival on nutrient supplemented media (I) 18. Describe the bases of Mendel`s experiments and bases for derivation of Mendel`s four principles. (II) 19. Explain the sum and product rules of probability. (II) 20. Use Punnett squares in monohybrid, dihybrid, and backcrosses to predict genotypic and phenotypic offspring ratios (II) 21. Use the branched-line method of predicting genotypic and phenotypic offspring ratios for multihybrid crosses. (II) 22. Identify differences among dominance, codominance, and incomplete dominance, and explain potential metabolic bases of each. (II) 23. Describe how various genetic phenomena modify expected Mendelian phenotypic ratios including the effects of codominance, incomplete dominance, multiple alleles, lethal alleles, epistasis, sex-linkage, modified dihybrid ratios, penetrance, and expressivity. (III) 24. Determine genetic mechanisms and propose metabolic pathways underlying modified expected Mendelian phenotypic ratios. (III) 25. Explain statistics behind Chi-square distribution and Chi- square analysis. (III) 26. Use Chi-square analysis in testing hypotheses regarding Mendelian ratios and modified Mendelian ratios. (III) 27. Describe the chromosome theory of inheritance. (IV) 28. Explain chromosome structure and organization (double-helix, histones, beads-on-a-string, nucleosomes, solenoid, looped domains, metaphase compaction). (IV) 29. Describe the cell cycle, including subphases of interphase and checkpoints. (IV) 30. Describe the process of mitosis and its phases, including major cellular events in each. (IV) 31. Describe the process of meiosis, its phases and the subphases of (or major events within) Prophase I, including major cellular events in each. (IV) 32. Describe linkage, basis of crossing-over, and molecular model of recombination. (IV) 33. Describe mechanisms of chromosomal sex-determination including dosage compensation, Y-chromosome mechanisms, and sex-chromosome balance. (IV) 34. Explain binomial distribution for calculating probabilities of exact phenotypic offspring ratios. (IV) 35. Explain the chromosomal basis of diseases of chromosome abnormalities (aneuploidy and polyploidy). (IV) 36. Describe macromutations of chromosome translocations and inversions; explain their effects on gamete production after crossing-over; describe potential effects of macromutations on evolution. (V) 37. Describe mechanisms of non-Mendelian inheritance, and identify hereditary patterns resulting from extranuclear inheritance, maternal effects, genomic imprinting, and infectious/parasitic inheritance. (VI) 38. Construct and interpret pedigrees, and distinguish hereditary patterns that would result from alleles that are autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive, Y-linked, and also due to non-Mendelian inheritance mechanisms. (VII) 39. Define linkage, and describe its effects on Mendelian expectations of independent assortment (VIII) 40. Use Chi-square analysis to test hypothesis of independent assortment. (VIII) 41. Determine classic map distances between gene loci using parental and crossover phenotypic ratios and three-point mapping analysis. (VIII) 42. Describe and draw the chromosomal models behind three-point mapping analysis, and explain interference and coefficient of coincidence. (VIII) 43. Describe structural properties of bacterial and bacteriophage genomes, and describe mapping techniques in bacteria and bacteriophages. (VIII) 44. Describe bases for positive and negative gene regulation mechanisms in prokaryotes. (IX) 45. Describe structure and function of prokaryotic operons such as lac- and trp-Operons. (IX) 46. Describe negative and positive control mechanisms, such as repressors, activators, glucose catabolite repression, aporepressor, and attenuation control. (IX) 47. Describe and analyze effects of mutations to components of lac- and trp-Operons. (IX) 48. Describe and analyze effects of partial diploids and cis- and trans-dominance in the lac-Operon (or similar) system. (IX) 49. Describe potential levels of control of gene expression / regulation due to complex structure and processes of eukaryotes. (IX) 50. Explain mechanisms of transcriptional control, including positive and negative regulatory elements and related transcription factors, regulatory enhancer/activator and silencer/repressor systems, structural motifs of regulator proteins, chromosome structure of transcriptionally active regions, galactose genes in yeast, and steroid hormone regulation in animals. (IX) 51. Describe mechanisms of mRNA processing control (alternative splicing). (IX) 52. Describe mechanisms of mRNA translational control, mRNA degradation control, and protein degradation control. (IX) 53. Describe several model systems of developmental genetics and cell-gene and gene-gene mechanisms involved including binary switch genes, cytoplasmic localization \226 gene interaction, zygotic genes, and cell-cell-gene interaction. (X) 54. Describe the role of programmed cell death in development. (X) 55. Describe Hardy-Weinberg Equilibrium principles and equation, and interpret term definitions for two and more alleles. (XI) 56. Estimate allele frequencies using Hardy-Weinberg equation. (XI) 57. Analyze and use models of evolutionary change under violation of each of the five assumptions necessary to maintain Hardy- Weinberg Equilibrium. (XI) 58. Describe hypothetical mechanisms behind unusual disease allele frequencies, such as sickle-cell anemia, CTFR-NBD1, and CCR5-?32. (XI) 59. Contrast continuous versus discontinuous traits and potential sources of phenotypic variation including number of loci, pleiotropy, epistasis, penetrance, expressivity, and components of total phenotypic variation. (XII) 60. Describe polygenic trait and additive allele effects on phenotypic distribution in a population. (XII) 61. Explain statistics of normal distribution, including statistics of central tendency, variance, standard deviation, and understanding of hypothesis testing using normal distributions. (XII) 62. Estimate number of genes affecting a trait, using results of F2 offspring phenotypic ratios. (XII) 63. Solve problems using concepts of broad-sense and narrow-sense heritability. (XII) 64. Describe potential genetic determinants of behavior and limits thereof, and explain how the number of loci influencing behavior predicts different hereditary patterns. (XIII) 65. Describe examples of behaviors determined by single locus / few loci and by more quantitative mechanisms. (XIII) 66. Describe bases for genetic transformation of species and divergence of conspecific populations. (XI, XIV) 67. Calculate genetic estimates of population structure, such as heterozygosity and Wright`s F-statistics. (XIV) 68. Contrast different definitions of species and limitations of each. (XIV) 69. Explain methods of reconstructing evolutionary history based upon cladistics, molecular clocks, and general phylogenetics. (XIV)
MCCCD Official Course Competencies must be coordinated with the content outline so that each major point in the outline serves one or more competencies. MCCCD faculty retains authority in determining the pedagogical approach, methodology, content sequencing, and assessment metrics for student work. Please see individual course syllabi for additional information, including specific course requirements.

MCCCD Official Course Outline
I. DNA and Gene Expression A. DNA as the hereditary material 1. Griffith 2. Hershey-Chase B. DNA structure \226 Watson and Crick model C. DNA replication 1. Meselson-Stahl 2. Prokaryotic a. Physical/molecular steps in process (1)\nDN. Proteins and enzymes involved at each step c. Function and structure of DNA polymerases and their subcomponents d. Semi-conservative process of polymerization e. Analytical skills to determine effects of non-function mutations occurring in the enzymatic subcomponents of DNA polymerases 3. Eukaryotic a. Physical/molecular steps in process (1)\nDN. Proteins and enzymes involved at each step c. Function and structure of DNA polymerases and their subcomponents d. Semi-conservative process of polymerization e. Analytical skills to determine effects of non-function mutations occurring in the enzymatic subcomponents of DNA polymerases D. Central dogma of gene expression E. Transcription 1. Prokaryotic a. Initiation (1)\nPr. Elongation, catalyzing phosphodiester bonds between ribonucleoside triphosphates and existing 3`-OH end of RNA polymer c. Termination (1)\nrh. Eukaryotic a. Initiation (1)\nPr. Elongation (1)\nCa. Termination, lack of DNA consensus termination sequence 3. mRNA structure 4. mRNA editing in eukaryotes a. 5` 7-methylguanosine cap b. 3` poly-A tail (associated with AAUAAA sequence) and molecular mechanism c. Exons and introns (5` GU . . . AG 3`) d. Spliceosomes (snurps and molecular model of spliceosome function) e. Ribozymes (self-editing introns) f. Substitution and insertion/deletion editing g. Alternative exon splicing F. Translation 1. Transcription and specificity of charging tRNAs: Aminoacyl-tRNA synthetases, ATP mediated formation of aminoacyl-AMP (amino-acid + AMP), synthetase bonding switch from amino-acid from AMP to tRNA creating amino 2. Prokaryotic a. Initiation (1)\nFo. N/A (3)\nSh. Elongation (1)\nGe. Termination: stop codon signaling of GTP-dependent release factor actions, polypeptide cleavage from terminal tRNA, disassociation of small and large subunits of ribosome. 3. Eukaryotic a. Initiation (1)\nFo. Elongation: eEf-2 / GTP mediated translocation c. Termination 4. Signal sequences and distribution of gene products post- translation G. Gene control of proteins, protein structure and levels thereof H. Effects of mutations 1. Point mutations and translation 2. Frameshift mutations and translation I. Metabolic pathways 1. Study of metabolic pathways using mutant strains 2. Enzymatic / allelic basis of pathways 3. Analysis of effects of non-function mutations of enzymes II. Mendelian Genetics A. Mono- and dihybrid crosses B. Experimental design behind and basis for derivation of Mendel`s four principles C. Derivation of expected genotypic and phenotypic ratios using Punnett squares D. Product rule of probability E. Multihybrid crosses \226 forked line method of deriving phenotypic and genotypic crosses F. Molecular basis for dominance / codominance / incomplete dominance III. Extensions and Exceptions to Mendelian Genetics: Modifications to Expected Mendelian Ratios and Molecular Bases and Potential Metabolic Pathways Behind Observed Ratios A. Codominance B. Incomplete dominance C. Three or more alleles D. Lethal alleles E. Epistasis F. Modified dihybrid ratios G. Sex-linkage H. Penetrance and expressivity I. X(squared) analysis and statistics behind analytic method IV. Mitosis and Meiosis A. Chromosome theory of inheritance 1. Chromosome structure and compaction organization 2. Cell cycle B. Processes of cell division, phases, subphases and major events within each C. Homology search, crossing-over, basis of linkage, molecular model of recombination D. Genotypic sex determination 1. Dosage compensation 2. Y-chromosome mechanisms 3. Sex-chromosome balance E. Binomial distribution and calculating probability of exact phenotypic (gender) ratios F. Diseases of chromosome abnormalities (aneuploidy, polyploidy) V. Macromutations: Effects on Gamete Production and Cross-Over Events A. Translocations B. Inversions C. Evolution and macromutations (human-chimpanzee karyotypes) VI. Non-Mendelian Mechanisms of Inheritance and Known Molecular Bases Behind Observed Phenotypic Patterns A. Extranuclear inheritance B. Maternal effects C. Genomic imprinting VII. Pedigree Analysis A. Conventions for constructing a pedigree including (but not limited to) designations for generations, individuals, gender, affected vs. unaffected individuals, carriers, consanguineous matings, propositus/a. B. Analytic skills to distinguish between expected inheritance patterns resulting from: 1. Autosomal dominant alleles 2. Autosomal recessive alleles 3. X-linked dominant alleles 4. X-linked recessive alleles 5. Y-linked alleles 6. Extranuclear inheritance 7. Maternal effects 8. Genomic imprinting VIII. Linkage and Mapping A. Eukaryotic 1. Definition of linkage 2. Effects of linkage on expected Mendelian ratios (under principles of independent assortment) 3. ?2 analysis against null hypothesis of Mendelian independent assortment 4. Mapping using (parental) hybrid crosses and mapping crosses (backcross to recessive parental line) a. Method of calculating map distances using parental and crossover phenotypic ratios b. Three-point crosses and map distance calculations based upon NCO, DCO, and SCO phenotypic ratios c. Chromosomal (visual) models behind mapping crosses d. Interference and coefficient of coincidence (3-point mapping) e. Complementation and complementation analysis B. Bacteria and bacteriophages 1. Bacterial conjugation and gene transfer (F factor, episomes) 2. Using different Hfr (episomic) strains to construct maps 3. Gene mapping through transformation 4. Phage genome structure 5. Gene mapping through transduction 6. Gene mapping in bacteriophages (crossover between different parental bacteriophages) 7. Complementation and complementation analysis C. Mapping and computer databases IX. Gene Regulation A. Feedback loops B. Bases for positive and negative gene regulation mechanisms and understanding of specific examples of each 1. Prokaryotic a. Lac Operon (1)\nOp. Trp Metabolism (1)\nOp. Eukaryotic a. Potential levels of control due to eukaryotic cell structure and function b. Transcriptional control (1)\nRe. N/A (6)\nSp. mRNA processing control (alternative splicing) d. mRNA translation control e. mRNA degradation control f. protein degradation control X. Developmental Genetics A. Binary switch genes B. Cytoplasmic localization and embryonic development (Drosophila model) C. Zygotic genes and zygote development (Drosophila model) 1. Gap genes 2. Pair-Rule genes 3. Segment polarity genes 4. Selector genes D. Cell-cell-gene interactions (C. elegans model) E. Programmed cell death XI. Population Genetics A. History B. Hardy-Weinberg Principles (two or more alleles) C. Estimating allele frequencies with HWE equation D. Evolutionary models and mathematical / conceptual problem solving based on violation of HWE principles 1. Immigration / emigration 2. Selection 3. Mutation 4. Random mating 5. Limited population size E. Disease allele frequencies and human selection models 1. Sickle-cell anemia 2. CTFR \226 cystic fibrosis 3. CCR5-?32\227HIV resistance allele / mutation XII. Quantitative Genetics A. Continuous vs. discontinuous trait values B. Sources of phenotypic variation 1. Single locus / few loci causes 2. Pleiotropy 3. Epistasis 4. Penetrance 5. Expressivity 6. VE, VG, VI, etc. C. Polygenic traits, additive alleles and derivation of normal distributions D. Basic statistics of the normal distribution 1. Statistics of central tendency 2. Variance, standard deviation 3. Explication of hypothesis testing using normal distribution (t-test) E. Estimating the number of genes affecting an additive trait F. Theoretical bases for, calculation of, and problems solving with heritability 1. Broad-sense 2. Narrow-sense XIII. Genetics and Behavior A. Potential determinants of behavior 1. Genetic a. Few loci b. Quantitative traits c. Environment d. Penetrance and expressivity B. Single-loci / few-loci behavioral examples C. Polygenic examples XIV. Evolution and Genetics A. Transformation of species and divergence of populations B. Measuring species and population differences and population structure 1. Heterozygosity 2. F-statistics C. Speciation 1. Definitions and limitations thereof 2. Mechanisms and possible examples D. Methods of estimating evolutionary trees (reconstructing evolutionary history) 1. Molecular clocks 2. Introduction to phylogenetics

MCCCD Governing Board Approval Date: 2/22/2005

All information published is subject to change without notice. Every effort has been made to ensure the accuracy of information presented, but based on the dynamic nature of the curricular process, course and program information is subject to change in order to reflect the most current information available.